"plain xs" works for gettin %ENV changes reflected ; I never cared much for swig
Are you sure it's really related to xs vs swig and not Linux vs Windows? Did you test your code under Windows?
Windows manages two sets of environment definitions as soon as the CRT is started which leads to consistency problems such as the one I encountered, but it's not specific to perl (cf http://www.codeproject.com/Articles/43029/When-what-you-set-is-not-what-you-get-SetEnvironme)

For the record, here is the workaround I came up with for now:

if($^O eq 'MSWin32') {
  require Win32::API;
  Win32::API->Import('msvcrt', 'int __cdecl _putenv (char* envstring)'
+);
}

sub exportEnvVar {
  my $envVar=shift;
  my $envVarDef="$envVar=".($ENV{$envVar}//'');
  die "Unable to export environment variable definition \"$envVarDef\"
+" unless(_putenv($envVarDef) == 0);
}
[download]

Then, when my script runs under Windows, I call exportEnvVar for each environment variable I update which needs to be seen by the dynamic library. This adds yet another platform-specific code to my script but I guess it's unavoidable... On Linux I don't need to do all that but on the other hand I need to restart (exec self) when I update LD_LIBRARY_PATH to select the dynamic library.